12-62389649-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_001252078.2(USP15):c.1602C>T(p.Phe534Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000837 in 1,612,836 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001252078.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USP15 | ENST00000280377.10 | c.1602C>T | p.Phe534Phe | synonymous_variant | Exon 13 of 22 | 1 | NM_001252078.2 | ENSP00000280377.5 | ||
USP15 | ENST00000353364.7 | c.1515C>T | p.Phe505Phe | synonymous_variant | Exon 12 of 21 | 1 | ENSP00000258123.4 | |||
USP15 | ENST00000549268.1 | n.960C>T | non_coding_transcript_exon_variant | Exon 6 of 7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000988 AC: 15AN: 151858Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000638 AC: 16AN: 250754Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135564
GnomAD4 exome AF: 0.0000821 AC: 120AN: 1460978Hom.: 0 Cov.: 32 AF XY: 0.0000826 AC XY: 60AN XY: 726806
GnomAD4 genome AF: 0.0000988 AC: 15AN: 151858Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74122
ClinVar
Submissions by phenotype
USP15-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at